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Title: A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples.
Author: Esteve Codina, Anna
Arpi, Oriol
Martínez-García, María
Pineda, Estela
Mallo, Mar
Gut, Marta
Carrato, Cristina
Rovira, Anna
López, Raquel
Tortosa i Moreno, Avelina
Dabad, Marc
Barco, Sonia del
Heath, Simon C.
Bagué, Silvia
Ribalta Farrés, Teresa María
Alameda, Francesc
Iglesia, Núria de la
Balaña, Carmen
Keywords: RNA
Mapatge cromosòmic humà
Human gene mapping
Issue Date: 25-Jan-2017
Publisher: Public Library of Science (PLoS)
Abstract: The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF) tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE) tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved.
Note: Reproducció del document publicat a:
It is part of: PLoS One, 2017, vol. 12, num. 1, p. e0170632
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ISSN: 1932-6203
Appears in Collections:Articles publicats en revistes (IDIBAPS: Institut d'investigacions Biomèdiques August Pi i Sunyer)
Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))
Articles publicats en revistes (Infermeria Fonamental i Medicoquirúrgica)
Articles publicats en revistes (Fonaments Clínics)

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